Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion

Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers

Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.

Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities

Ribonucleic acids (RNAs) play essential roles in living cells. Many of them fold into defined three-dimensional (3D) structures to perform functions. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determinations of RNA to atomic resolutions. However, most RNA molecules are structurally flexible, limiting the resolution of their structures solved by cryo-EM. In modeling these molecules, several computational methods are limited by the requirement of massive computational resources and/or the low efficiency in exploring large-scale structural variations. Here we use hierarchical natural move Monte Carlo (HNMMC), which takes advantage of collective motions for groups of nucleic acid residues, to refine RNA structures into their cryo-EM maps, preserving atomic details in the models. After validating the method on a simulated density map of tRNA, we applied it to objectively obtain the model of the folding intermediate for the specificity domain of ribonuclease P from Bacillus subtilis and refine a flexible ribosomal RNA (rRNA) expansion segment from the Mycobacterium tuberculosis (Mtb) ribosome in different conformational states. Finally, we used HNMMC to model atomic details and flexibility for two distinct conformations of the complete genomic RNA (gRNA) inside MS2, a single-stranded RNA virus, revealing multiple pathways for its capsid assembly.

Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water

The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water.

Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components

Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P.

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg(2+) concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg(2+) concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.

Many-body effect in ion binding to RNA

Ion-mediated electrostatic interactions play an important role in RNA folding stability. For a RNA in a solution with higher Mg(2+) ion concentration, more counterions in the solution can bind to the RNA, causing a strong many-body coupling between the bound ions. The many-body effect can change the effective potential of mean force between the tightly bound ions. This effect tends to dampen ion binding and lower RNA folding stability. Neglecting the many-body effect leads to a systematic error (over-estimation) of RNA folding stability at high Mg(2+) ion concentrations. Using the tightly bound ion model combined with a conformational ensemble model, we investigate the influence of the many-body effect on the ion-dependent RNA folding stability. Comparisons with the experimental data indicate that including the many-body effect led to much improved predictions for RNA folding stability at high Mg(2+) ion concentrations. The results suggest that the many-body effect can be important for RNA folding in high concentrations of multivalent ions. Further investigation showed that the many-body effect can influence the spatial distribution of the tightly bound ions and the effect is more pronounced for compact RNA structures and structures prone to the formation of local clustering of ions.

A novel implicit solvent model for simulating the molecular dynamics of RNA

Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin-Debye model and the Poisson-Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.

Insights into the regulatory landscape of the lysine riboswitch

A prevalent means of regulating gene expression in bacteria is by riboswitches found within mRNA leader sequences. Like protein repressors, these RNA elements must bind an effector molecule with high specificity against a background of other cellular metabolites of similar chemical structure to elicit the appropriate regulatory response. Current crystal structures of the lysine riboswitch do not provide a complete understanding of selectivity as recognition is substantially mediated through main-chain atoms of the amino acid. Using a directed set of lysine analogs and other amino acids, we have determined the relative contributions of the polar functional groups to binding affinity and the regulatory response. Our results reveal that the lysine riboswitch has >1000-fold specificity for lysine over other amino acids. The aptamer is highly sensitive to the precise placement of the ε-amino group and relatively tolerant of alterations to the main-chain functional groups in order to achieve this specificity. At low nucleotide triphosphate (NTP) concentrations, we observe good agreement between the half-maximal regulatory activity (T(50)) and the affinity of the receptor for lysine (K(d)), as well as many of its analogs. However, above 400 μM [NTP], the concentration of lysine required to elicit transcription termination rises, moving into the riboswitch into a kinetic control regime. These data demonstrate that, under physiologically relevant conditions, riboswitches can integrate both effector and NTP concentrations to generate a regulatory response appropriate for global metabolic state of the cell.

Cooperative tertiary interaction network guides RNA folding

Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

SAXS studies of ion-nucleic acid interactions

Positively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.

Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA

There are potentially several ways Mg2+ might promote formation of an RNA tertiary structure: by causing a general "collapse" of the unfolded ensemble to more compact conformations, by favoring a reorganization of structure within a domain to a form with specific tertiary contacts, and by enhancing cooperative linkages between different sets of tertiary contacts. To distinguish these different modes of action, we have studied Mg2+ interactions with the adenine riboswitch, in which a set of tertiary interactions that forms around a purine-binding pocket is thermodynamically linked to the tertiary "docking" of two hairpin loops in another part of the molecule. Each of four RNA forms with different extents of tertiary structure were characterized by small-angle X-ray scattering. The free energy of interconversion between different conformations in the absence of Mg2+ and the free energy of Mg2+ interaction with each form have been estimated, yielding a complete picture of the folding energy landscape as a function of Mg2+ concentration. At 1 mM Mg2+ (50 mM K+), the overall free energy of stabilization by Mg2+ is large, -9.8 kcal/mol, and about equally divided between its effect on RNA collapse to a partially folded structure and on organization of the binding pocket. A strong cooperative linkage between the two sets of tertiary contacts is intrinsic to the RNA. This quantitation of the effects of Mg2+ on an RNA with two distinct sets of tertiary interactions suggests ways that Mg2+ may work to stabilize larger and more complex RNA structures.

Time resolved SAXS and RNA folding

Small angle X-ray scattering provides low resolution structural information about macromolecules in solution. When coupled with rapid mixing methods, SAXS reports time-dependent conformational changes of RNA induced by the addition of Mg(2+) to trigger folding. Thus time-resolved SAXS provides unique information about the global or overall structures of transient intermediates populated during folding. Notably, SAXS provides information about the earliest folding events, which can evade detection by other methods.

Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number

Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17–174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 × 10⁻¹⁰ N^−0.39 m² s⁻¹. The hydrodynamic radius R_H depended on N with R_H = 5.00 × 10⁻¹⁰N^0.38 m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 ± 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size.

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Of proteins and RNA: the RNase P/MRP family

Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.